By Dr. Mercola

Your body houses some 100 trillion bacteria, and about 1 quadrillion viruses (bacteriophages). In essence, we’re little more than walking microbe colonies, seeing how these bacteria outnumber your cells 10 to 1, and the bacteriophages in turn outnumber bacteria 10 to 1.

These organisms perform a wide variety of functions, and we’ve now come to realize that they need to be properly balanced and nourished if we want to maintain good physical and mental health.

While the Human Genome Project (HGP) was expected to result in gene-based therapies to more or less rid us of disease, it actually revealed that your genetic makeup plays a much smaller role than anyone imagined.

Your genes, as it turns out, are only responsible for about 10 percent of diseases.¹

The remaining 90 percent are induced by environmental factors, and researchers are now realizing that your microbiome may be among the most important factors, as genes are turned on and off depending on which microbes are present!

Emerging science also shows that your microbiome can be rapidly altered, for better or worse, based on factors such as diet, lifestyle, and chemical exposures.

This is a double-edged sword, no doubt, considering how many of our modern conveniences (such as processed foods, antibiotics, and pesticides) turn out to be extremely detrimental to our gut flora.

On the other hand, your diet is one of the easiest, fastest, and most effective ways to improve and optimize your microbiome. So the good news is that you have a great degree of control over your health destiny.

Human DNA Contains Microbial Genes

Remarkably, some of the most recent research suggests bacteria may even have played a role in the diversification and alteration of human DNA, by way of horizontal gene transfer.^{2 , 3}

According to researchers, potentially hundreds of microbial genes have slipped into our DNA over the course of mankind’s history, including genes that help your immune system defend itself against infections. It’s possible other genes helped mankind adapt to changing diets and environmental conditions.

It seems not a month goes by without new revelations about how bacteria influence our lives. Here, I’ll review some of the most recent findings gaining more widespread acknowledgment.

How Gut Bacteria Influence Your Weight

Bacteria appear to influence human health and disease in two key ways. While an overabundance of certain bacteria have been linked to various diseases, other microbes appear to be actively involved in preventing certain disease states.

When they’re lacking, you end up losing this protection, which allows the disease process to set in.

For example, by eradicating four species of bacteria (Lactobacillus, Allobaculum, Rikenelleceae, and Candidatus arthromitus), researchers were able to trigger metabolic changes in lab animals that led to obesity.⁴

As time goes on, it seems increasingly reasonable to think that obesity is largely influenced by gut bacteria. This in no way changes the fact that certain foods will make you pack on the pounds, the bacteria just play a major role in facilitating that process.

The foods known to produce metabolic dysfunction and insulin resistance (such as processed foods, fructose/sugar, and artificial sweeteners) also decimate beneficial gut bacteria, and it may well be that this is a key mechanism by which these foods promote obesity.

Chemicals may also contribute to your weight problem by way of your gut microbiome.

For example, a study⁵ published in the July issue of Environmental Health Perspectives found that persistent organic pollutants (POPs) found in food altered the gut microbiome in mice, thereby contributing to the development of obesity and metabolic dysfunction.

Another study^6,7 found that one microbe called Akkermansia muciniphila helps ward off obesity, diabetes, and heart disease by lowering blood sugar, improving insulin resistance, and promoting a healthier distribution of body fat.

A. muciniphila is associated with a fiber-rich diet, and fiber has long been recognized for its beneficial effects on health and weight. It’s still not known whether A. muciniphila produces these effects all on its own, or whether it helps promote other beneficial bacteria, however.

According to the authors:

“Our findings demonstrate the need for further investigation to ascertain the therapeutic applicability of A. muciniphila in the treatment of insulin resistance.

A. muciniphila may be identified as a diagnostic or prognostic tool to predict the potential success of dietary interventions.”

Fiber-Digesting Bacteria Also Influence Your Immune Function

Previous research has also shown that gut microbes specializing in fermenting soluble fiber play an important role in preventing inflammatory disorders, as they help calibrate your immune system.⁸

Specifically, the byproducts of this fermenting activity help nourish the cells lining your colon, thereby preventing leaky gut — a condition in which toxins are allowed to migrate from your gut into your blood stream.

The inflammatory response actually starts in your gut and then travels to your brain, which subsequently sends signals to the rest of your body in a complex feedback loop.

So in order to address chronic inflammation and inflammatory diseases, it’s important to nourish your gut flora with the right foods. Examples include traditionally fermented foods and raw foods, and especially those high in fiber.

Sugar, on the other hand, feeds fungi that produce yeast infections and sinusitis. Researchers have also linked high-sugar diets to memory – and learning impairments, courtesy of altered gut bacteria.^9,10 According to lead author Dr. Kathy Magnusson:¹¹

“We’ve known for a while that too much fat and sugar are not good for you.  This work suggests that fat and sugar are altering your healthy bacterial systems, and that’s one of the reasons those foods aren’t good for you. It’s not just the food that could be influencing your brain, but an interaction between the food and microbial changes.” [Emphasis mine]

Fiber and Fermented Foods Are Key Components of a Healthy Diet

While it’s virtually impossible to determine the composition of an ideal microbiome, seeing how our gut flora is as individual as our finger print, what we do know is that a healthy diet is key for optimizing your individual microbiome. We’ve also come to realize that fermented foods and foods high in fiber are very important components of a healthy diet, as these foods help nourish a wide variety of beneficial bacteria.

Such foods have been part of the human diet since ancient times, and replacing them with chemically altered and “sterilized” processed foods has led to many of our current health problems. Traditional sauerkraut, for example, has been identified as a heart-healthy superfood. As reported by The Epoch Times:¹²

“Research in the medical journal Food and Function¹³found that unpasteurized sauerkraut contained a potent probiotic known as wild lactobacillus plantarum FC225, to which many of sauerkraut’s heart-healing abilities could be attributed. Upon investigation, the scientists conducting the study found that the probiotic-rich sauerkraut helped in the following ways:

•Reduced cholesterol levels

•Reduced triglyceride levels

•Significantly increased levels of two powerful antioxidants known as superoxide disumutase (SOD) and glutathione

•Decreased the degradation of fats in the body (a process known as lipid peroxidation)”

New Research Shows How Much Fiber Different Diets Provide

American Gut Project is the largest, open source and crowd funded microbiome project in the world. Below is a box-and-whisker plot of the results. Their research¹⁴ has collected data from over 5,000 patients who have submitted samples and dietary questionnaires. They’ve been able to calculate the fiber and the median daily fiber intake for various dietary groups, which is as follows:

• Paleo-Like: 19 g/day
• Omnivore: 19 g/day
• Paleo: 25.1 g/day
• Omnivore, but no red meat: 27.8 g/day
• Vegetarian: 32.8 g/day
• Vegan: 43 g/day

Are You Getting Enough Fiber and Fermented Foods in Your Diet?

Ideally, include a variety of fermented foods and beverages in your diet, because each food will inoculate your gut with a mix of different microorganisms. There are many fermented foods you can easily make at home, including:

• Fermented vegetables, including pureed baby foods
• Chutneys
• Condiments, such as salsa and mayonnaise
• Cultured dairy, such as yogurt, kefir, and sour cream
• Fish, such as mackerel and Swedish gravlax

As for fiber, dietary guidelines call for 20 to 30 grams of fiber per day. I believe an ideal amount for most adults is likely much higher, perhaps twice as much. Many whole foods, especially fruits and vegetables, naturally contain both soluble and insoluble fiber.

This is ideal, as both help feed the microorganisms living in your gut. So to maximize your health benefits, focus on eating more vegetables, nuts, and seeds. Following is a small sampling of foods that contain high levels of soluble and insoluble fiber.

I am a major fan of fiber especially soluble fibers like psyllium as they not only serve as a prebiotic for your microbiome but are also metabolized to short chain fatty acids like butyrate, propionic and acetate that nourish your colonic cells. They are also converted to ketones that nourish your tissues.

I personally consume nearly 100 grams of fiber a day and about 2 tablespoons of organic psyllium three times a day that provides about 25 grams of soluble fiber. The other 75 percent of my fiber comes primarily from vegetables and seeds.

Psyllium seed husk, flax, and chia seeds	Berries	Vegetables such as broccoli and Brussels sprouts
Root vegetables and tubers, including onions, sweet potatoes, and jicama	Almonds	Peas
Green beans	Cauliflower	Beans

Swapping Gut Bacteria May Help Reverse Type 2 Diabetes

Type 2 diabetes is another common health problem that can be traced back to impaired gut flora. Studies have found that the microbial composition in diabetics differ from non-diabetics. In particular, diabetics tend to have fewer Firmicutes and more plentiful amounts of Bacteroidetes and Proteobacteria, compared to non-diabetics. A positive correlation for the ratios of Bacteroidetes to Firmicutes and reduced glucose tolerance has also been found.

A researcher in Amsterdam, Dr. Max Nieuwdorp, has published a number of studies looking at changes in the microbiome that are characteristic of type 2 diabetes. In one trial, he was able to reverse type 2 diabetes in all of the 250 study participants by doing fecal transplantations on them. Remarkable as it may sound, by changing the makeup of the gut bacteria, the diabetes was resolved.

Even more interesting, type 1 diabetes (insulin dependent) in young children also tends to be preceded by a change in gut bacteria. This makes sense as your gut flora control about 80 percent of your immune response and type 1 diabetes is an autoimmune disease. The good news is that researchers have found that certain microbes can actually help prevent type 1 diabetes, suggesting your gut flora may indeed be an epigenetic factor that plays a significant role in this condition.

Your Gut Is Your Second Brain

The quality, quantity, and composition of the bacteria in your gut have enormous influence on your brain. For example, studies^15,16 have found that autistic children have distinctly different microbiome compared to healthy children. Notably, they tend to have fewer beneficial bacteria such as Bifidobacterium.

Addressing such imbalances is the core component of the GAPS nutritional program, created by Dr. Natasha Campbell-McBride, who believes “healing and sealing” the gut is paramount for those with neurological dysfunction, including autism. Dr. David Perlmutter also explores the connection between gut health and degenerative brain disorders such as Alzheimer’s in his new book, “Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain for Life.”

This again goes back to the fact that gut microbes help maintain the integrity of your gut lining. As explained by Dr. Perlmutter,¹⁷many of the factors that affect permeability of the blood-brain barrier are similar to those that affect the gut, which is why leaky gut can lead to neurological diseases as easily as it can manifest as some other form of autoimmune disorder.

The permeability of your gut lining can be measured by looking at a chemical called lipopolysaccharide (LPS), which is the covering over certain groups of bacteria in your gut. When you have higher levels of antibodies against LPS in the bloodstream, it’s a marker of leaky gut. LPS is also in and of itself a powerful instigator of the inflammatory cascade.

Higher levels of LPS in the blood dramatically increase inflammation throughout your body, including your brain. Alzheimer’s and Lou Gehrig’s disease, for example, are both correlated with dramatically elevated levels of LPS.

Mood Disorders May Be Rooted in Impaired Microbiome Too

Not only can impairments in your microbiome promote neurological diseases, it can also have a powerful impact on your general mood. Depression is increasingly starting to be viewed as a symptom of poor gut health, and therein may lie the real cure as well … For example, in one recent study^{18 ,19,20}researchers found that fermented foods and drinks helped curb social anxiety disorder in young adults.

Previous trials have also demonstrated that probiotics can help ease both anxiety and depression.  For example, one study²¹ found that the probiotic Lactobacillus rhamnosus had a marked effect on GABA levels — an inhibitory neurotransmitter that is significantly involved in regulating many physiological and psychological processes — in certain brain regions and lowered the stress-induced hormone corticosterone, resulting in reduced anxiety- and depression-related behavior.

In another study,²² people who took a multi-strain probiotic for at least four weeks reported a lessening of rumination — recurring, persistent thoughts about something distressing that has or may happen, which tends to create anxiety. Another recent study^23,24 found that high-glycemic foods (including those high in refined grains and added sugar) were associated with higher odds of depression.

While it didn’t look at the role of bacteria, the link between high-sugar diets and alterations in gut bacteria has been established in other studies, including the one mentioned earlier, in which these microbial changes led to cognitive impairments such as learning difficulties and worsened memory.

As discussed in The New York Times,²⁵researchers are now investigating a number of psychoactive compounds found in feces, and are experimenting with fecal transplants in animals to assess its effect on neurodevelopment:

“Anxiety, depression and several pediatric disorders, including autism and hyperactivity, have been linked with gastrointestinal abnormalities … [L]ast September, the National Institute of Mental Health awarded four grants worth up to $1 million each to spur new research on the gut microbiome’s role in mental disorders, affirming the legitimacy of a field that had long struggled to attract serious scientific credibility … It seems plausible, if not yet proved, that we might one day use microbes to diagnose neurodevelopmental disorders, treat mental illnesses and perhaps even fix them …”.

Optimizing Your Microbiome Is a Potent Disease Prevention Strategy

I believe optimizing your gut flora may be one of the most important things you can do for your health, and here you can wield your personal power to the fullest by making healthy food and medical choices. Not only can optimizing your gut health help normalize your weight and ward off diabetes, it’s also a critical component for a well-functioning immune system, which is your primary defense against virtually all disease.

You will be pleased to know that supporting your microbiome isn’t very complicated. However, you do need to take proactive steps to implement certain key strategies while actively avoiding other factors. To optimize your microbiome both inside and out, consider the following recommendations:

Eat plenty of fermented foods. Healthy choices include lassi, fermented grass-fed organic milk such as kefir, natto (fermented soy), and fermented vegetables. If you ferment your own, consider using a special starter culture that has been optimized with bacterial strains that produce high levels of vitamin K2. This is an inexpensive way to optimize your K2, which is particularly important if you’re taking a vitamin D3 supplement.	Antibiotics, unless absolutely necessary (and when you do, make sure to reseed your gut with fermented foods and/or a probiotic supplement). And while some researchers are looking into methods that might help ameliorate the destruction of beneficial bacteria by antibiotics,26,27 your best bet is likely always going to be reseeding your gut with probiotics from fermented and cultured foods and/or a high-quality probiotic supplement.
Take a probiotic supplement. Although I’m not a major proponent of taking many supplements (as I believe the majority of your nutrients need to come from food), probiotics are an exception if you don’t eat fermented foods on a regular basis	Conventionally-raised meats and other animal products, as CAFO animals are routinely fed low-dose antibiotics, plus genetically engineered grains loaded with glyphosate, which is widely known to kill many bacteria.
Boost your soluble and insoluble fiber intake, focusing on vegetables, nuts, and seeds, including sprouted seeds.	Chlorinated and/or fluoridated water. Especially in your bathing such as showers, which are worse than drinking it.
Get your hands dirty in the garden. Germ-free living may not be in your best interest, as the loss of healthy bacteria can have wide-ranging influence on your mental, emotional, and physical health. Exposure to bacteria and viruses can serve as “natural vaccines” that strengthen your immune system and provide long-lasting immunity against disease. Getting your hands dirty in the garden can help reacquaint your immune system with beneficial microorganisms on the plants and in the soil. According to a recent report,28 lack of exposure to the outdoors can in and of itself cause your microbiome to become “deficient.”	Processed foods. Excessive sugars, along with otherwise “dead” nutrients, feed pathogenic bacteria. Food emulsifiers such as polysorbate 80, lecithin, carrageenan, polyglycerols, and xanthan gum also appear to have an adverse effect on your gut flora.29 Unless 100% organic, they may also contain GMO’s that tend to be heavily contaminated with pesticides such as glyphosate. Artificial sweeteners have also been found to alter gut bacteria in adverse ways.30
Open your windows. For the vast majority of human history the outside was always part of the inside, and at no moment during our day were we ever really separated from nature. Today, we spend 90 percent of our lives indoors. And, although keeping the outside out does have its advantages it has also changed the microbiome of your home. Research31 shows that opening a window and increasing natural airflow can improve the diversity and health of the microbes in your home, which in turn benefit you.	Agricultural chemicals, glyphosate (Roundup) in particular is a known antibiotic and will actively kill many of your beneficial gut microbes if you eat and foods contaminated with Roundup
Wash your dishes by hand instead of in the dishwasher. Recent research has shown that washing your dishes by hand leaves more bacteria on the dishes than dishwashers do, and that eating off these less-than-sterile dishes may actually decrease your risk of allergies by stimulating your immune system.	Antibacterial soap, as they too kill off both good and bad bacteria, and contribute to the development of antibiotic-resistance.